The `with_apsimx` function automates the process of setting up and running APSIM Next Generation (NG) simulations in a temporary or specified folder. This approach helps reduce I/O overhead, particularly in high-performance computing (HPC) environments with network file systems (NFS). The frequent file I/O operations performed by APSIM NG (e.g., writing to SQLite databases) can strain file systems, and redirecting simulations to a local folder mitigates this issue. The function can also perform optional post-processing of the simulation results.
Arguments
- models
A character string specifying the path to the APSIM NG executable (`Models.exe` on Windows or `Models` on Linux).
- file
A character string specifying the path to the `.apsimx` simulation file.
- mets
A character vector specifying paths to meteorological data (`.met` files) used in the simulation. Currently, only `.met` files located in the same folder as the `.apsimx` file are supported (optional).
- target
A character string specifying the target directory where simulations will be run. Defaults to the R system temporary directory (`tempdir()`).
- clean
A character string specifying which files or directories to clean after the simulation. Options are:
`"none"`: No files are cleaned (default).
`"simulations"`: Cleans only simulation-related files (e.g., `*.apsimx`, `*.db`, `*.db-shm`, `*.db-wal`, `*.csv`).
`"mets"`: Cleans only meteorological files (e.g., `*.met`).
`"all"`: Cleans all files, including APSIM NG executable files, simulations, and meteorological files.
- post_process
An optional function for post-processing simulation results. The function must accept a `folder` argument specifying the directory containing the simulation results.
- ...
Additional arguments passed to both the `run_models` and `post_process` functions.
Value
If a `post_process` function is provided, its return value is returned. Otherwise, the function returns `NULL`.
See also
run_models: Runs APSIM simulations.
do.call: Dynamically calls functions with named arguments.
Examples
if (FALSE) { # \dontrun{
# Run simulations without post-processing
with_apsimx(
models = "path/to/apsimx",
file = "path/to/input.apsimx",
mets = c("path/to/met1.met", "path/to/met2.met"),
clean = "all"
)
# Run simulations with post-processing
post_process_function <- function(folder) {
output_files <- list.files(folder, full.names = TRUE)
message("Output files:", paste(output_files, collapse = "\n"))
}
result <- with_apsimx(
models = "path/to/apsimx",
file = "path/to/input.apsimx",
mets = c("path/to/met1.met", "path/to/met2.met"),
post_process = post_process_function
)
} # }